int writeStructureFile(int popid, int popnum)
{
int noidis = 0;
int tts=-1;
try
{
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
Query query = conn.query();
string pp = "pop"+toStrings(popnum);
query << "SELECT "<<pp<<" FROM structure WHERE popstructid = " << popid << " ORDER BY sampleid";
StoreQueryResult ares = query.store();
if(!ares)
{
cerr << query.error() << endl;
return -1;
}
else
{
ofstream myfile;
string fname = "data.test.Z";
myfile.open(fname.c_str());
tts = ares.num_rows();
for(size_t i = 0; i < ares.num_rows(); i ++)
{
myfile << ares[i][pp.c_str()] << "\n";
}
myfile.close();
}
}
catch(BadQuery er)
{
cerr << "Error: " << er.what() << endl;
return -1;
}
catch(const BadConversion& er)
{
cerr << "Conversion error: " << er.what() << endl;
return -1;
}
catch(const Exception& er)
{
cerr << "Error: " << er.what() << endl;
return -1;
}
return tts;
}
static bool handle_name_exists(const StoreQueryResult& result)
{
size_t rowCount = result.num_rows();
assert(rowCount < 2);
return rowCount == 1;
}
void createParmFiles2(string mask, int popid, int popno, int totaltrait, int totalmarker, string db, string name_str)
{
int distinctpop = -1;
try
{
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
Query query = conn.query();
string pp = "pop"+toStrings(popno);
//SELECT COUNT(DISTINCT pop1 ) as number FROM structure where popstructid = 1;
query << "SELECT COUNT(DISTINCT "<<pp<<" ) as number FROM structure WHERE popstructid = " << popid;
StoreQueryResult ares = query.store();
if(!ares)
{
cerr << query.error() << endl;
return;
}
else
{
for(size_t i = 0; i < ares.num_rows(); i ++)
{
distinctpop = ares[i]["number"] ;
}
}
}
catch(BadQuery er)
{
cerr << "Error: " << er.what() << endl;
return;
}
catch(const BadConversion& er)
{
cerr << "Conversion error: " << er.what() << endl;
return;
}
catch(const Exception& er)
{
cerr << "Error: " << er.what() << endl;
return;
}
ofstream myfile;
myfile.open("parms2.txt");
myfile <<mask<<" "<<popid<<" "<<popno<<" "<<totaltrait<<" "<<totalmarker<<" "<<name_str<<" "<<db<<" "<<distinctpop<< " " << team << endl;
myfile<<"vanilla"<<endl;
myfile.close();
}
/**
@brief Return the list of all orders of a given user
@param[in] pp An instance of User
@return A vector of Order
*/
vector<Order *> & Order::ordersForUser(User & pp)
{
vector<Order *> *orders = new vector<Order *>;
// get an instance of the database
Database& db = Database::instance();
try {
// ask Database for a valid connection to mySQL
Connection *conn = db.getConnection();
// obtain an instance of mysqlpp::Query and init it
Query q = conn->query();
q << "SELECT * FROM orders WHERE uid = " << pp.uniqueID()
<< " ORDER BY oid, date";
StoreQueryResult res = q.store();
if (!res.empty()) {
orders->reserve(res.num_rows());
StoreQueryResult::const_iterator it;
for (it = res.begin(); it != res.end(); it++){
Row row = *it;
orders->push_back(new Order(row));
}
}
} catch (std::exception &e) {
cerr << "an error occurred: " << e.what() << endl;
}
return *orders;
}
/**
@brief Returns the list of available categories.
@return Vector of pointer to Category
*/
vector<Category *> &Category::catalog()
{
// get an instance of the database
Database& db = Database::instance();
vector<Category *> *catalog = NULL;
try {
// ask Database for a valid connection to mySQL
Connection *conn = db.getConnection();
// obtain an instance of mysqlpp::Query and init it
Query q = conn->query(SQL_CATEGORY_CAT);
StoreQueryResult res = q.store();
if (!res.empty()) {
catalog = new vector<Category *>;
catalog->reserve(res.num_rows());
for (size_t i = 0; i < res.num_rows(); ++i) {
Category *c = new Category();
c->setValueForKey(KEY_CAT_CID,
(string) res[i][KEY_CAT_CID]);
c->setValueForKey(KEY_CAT_NAME,
(string) res[i][KEY_CAT_NAME]);
catalog->push_back(c);
}
}
}
catch (const mysqlpp::BadQuery& e) {
// Something went wrong with the SQL query.
cerr << "Query failed: " << e.what() << endl;
}
catch (const Exception& er) {
cerr << "Error: " << er.what() << endl;
}
return *catalog;
}
int db::get_station(std::string mac) {
StoreQueryResult res = q_get_station.store(mac.c_str(), "");
// found station
if (res.num_rows() > 0) {
mysqlpp::StoreQueryResult::const_iterator it;
mysqlpp::Row row = *(res.begin());
return row[0];
}
cerr << mac << endl;
// new station to db
SimpleResult r_exp = q_insert_station.execute("0", "0", mac.c_str());
return r_exp.insert_id();
}
/**
@brief Return the list of products of a given category
@param[in] aCid The category ID
@return A vector of ProductProxy
@note Pass zero as category ID to get all products
*/
vector<ProductProxy *> & ProductProxy::catalog(int aCid)
{
// get an instance of the database
Database& db = Database::instance();
vector<ProductProxy *> *catalog = NULL;
try {
// ask Database for a valid connection to mySQL
Connection *conn = db.getConnection();
// obtain an instance of mysqlpp::Query and init it
Query q = conn->query();
q << SQL_CATALOG_PROXY;
if (aCid != 0)
q << "WHERE cid = " << aCid;
q << " ORDER BY pid, category, name";
StoreQueryResult res = q.store();
if (!res.empty()) {
catalog = new vector<ProductProxy *>;
catalog->reserve(res.num_rows());
for (size_t i = 0; i < res.num_rows(); ++i) {
catalog->push_back(new ProductProxy((int) res[i][0]));
}
}
}
catch (const mysqlpp::BadQuery& e) {
// Something went wrong with the SQL query.
cerr << "Query failed: " << e.what() << endl;
}
catch (const Exception& er) {
cerr << "Error: " << er.what() << endl;
}
return *catalog;
}
int gettsid(string mask)
{
try
{
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
//cout << conn.error() << endl;
Query query = conn.query();
query << "SELECT get_ts_id('" << mask << "') as id";
StoreQueryResult ares = query.store();
if(!ares)
{
cerr << query.error() << endl;
return -1;
}
int id;
for(size_t i = 0; i < ares.num_rows(); i++)
{
id = ares[i]["id"];
return id;
}
}
catch(BadQuery er)
{
cerr<< "Error: " <<er.what() <<endl;
return -1;
}
catch(const BadConversion& er)
{
cerr <<"Conversion error: " << er.what() << endl;
return -1;
}
catch (const Exception& er)
{
cerr << "Error: " <<er.what() << endl;
return -1;
}
}
int main() {
try {
Connection conn(false);
conn.connect("map", "localhost", "root", "dtbs");
Query query = conn.query();
/* To insert stuff with escaping */
/* query << "INSERT INTO map " <<
"VALUES (" <<
"'', " << // This is left empty because the column is AUTO_INCREMENT
"\"" << escape << "some_var_that_contains_some_value" << "\"" <<
");";
query.execute();*/
/* That's it for INSERT */
/* Now SELECT */
query << "SELECT * FROM Station";
StoreQueryResult ares = query.store();
for (size_t i = 0; i < ares.num_rows(); i++)
cout << "Name: " << ares[i]["id"] << " - Address: " << ares[i]["name"] << endl;
/* Let's get a count of something */
query << "SELECT COUNT(*) FROM Station";
StoreQueryResult bres = query.store();
cout << "Total rows: " << bres[0]["id"];
} catch (BadQuery er) { // handle any connection or
// query errors that may come up
cerr << "Error: " << er.what() << endl;
return -1;
} catch (const BadConversion& er) {
// Handle bad conversions
cerr << "Conversion error: " << er.what() << endl <<
"\tretrieved data size: " << er.retrieved <<
", actual size: " << er.actual_size << endl;
return -1;
} catch (const Exception& er) {
// Catch-all for any other MySQL++ exceptions
cerr << "Error: " << er.what() << endl;
return -1;
}
return (EXIT_SUCCESS);
}
bool MasterServer::get_fileinfo(const string &fid, FileInfo &fileinfo)
{
//查找cache
map<string, FileInfo>::iterator it = m_fileinfo_cache.find(fid);
if(it != m_fileinfo_cache.end())
{
fileinfo = it->second;
return true;
}
//查找数据库
if(m_db_connection == NULL)
return false;
char sql_str[1024];
snprintf(sql_str, 1024, "select fid,name,size,chunkid,chunkip,chunkport,findex,foffset from SFS.fileinfo_%s where fid='%s'"
,fid.substr(0,2).c_str(), fid.c_str());
Query query = m_db_connection->query(sql_str);
StoreQueryResult res = query.store();
if (!res || res.empty())
return false;
size_t i;
for(i=0; i<res.num_rows(); ++i)
{
ChunkPath chunk_path;
fileinfo.fid = res[i]["fid"].c_str();
fileinfo.name = res[i]["name"].c_str();
fileinfo.size = atoi(res[i]["size"].c_str());
chunk_path.id = res[i]["chunkid"].c_str();
chunk_path.ip = res[i]["chunkip"].c_str();
chunk_path.port = atoi(res[i]["chunkport"].c_str());
chunk_path.index = atoi(res[i]["findex"].c_str());
chunk_path.offset = atoi(res[i]["foffset"].c_str());
fileinfo.add_chunkpath(chunk_path);
}
//添加到cache
m_fileinfo_cache.insert(std::make_pair(fileinfo.fid, fileinfo));
return true;
}
int getNextTaskId()
//searching for a task to start
{
int id = -1,progress;
ostringstream strbuf;
strbuf << "SELECT id,progress FROM tasks WHERE started=0 and running=0 ORDER BY date ASC LIMIT 1";
Connection con(use_exceptions);
try
{
Query query = con.query();
con.connect(DATABASE, HOST, USER, PASSWORD);
query << strbuf.str();
StoreQueryResult res = query.store();
cout<<strbuf.str()<<endl;
if (res && res.num_rows() > 0)
{
mysqlpp::Row row;
row = res.at(0);
id = row["id"];
progress = row["progress"];
}
}
catch (const BadQuery& er)
{
// Handle any query errors
cerr << "getNextTaskId - Query error: " << er.what() << endl;
id = -1;
}
catch (const BadConversion& er)
{
// Handle bad conversions
cerr << "getNextTaskId - Conversion error: " << er.what() << endl <<
"\tretrieved data size: " << er.retrieved <<
", actual size: " << er.actual_size << endl;
id = -1;
}
catch (const Exception& er)
{
// Catch-all for any other MySQL++ exceptions
cerr << "getNextTaskId - Error: " << er.what() << endl;
id = -1;
}
if(id>=1 && ! (progress >=1)) { //first time run, convert formula/density
try{
strbuf.str("");
strbuf << "SELECT energy,formula0,formula1,formula12,rhoin0,rhoin1,rhoin12 FROM tasks WHERE id="<<id;
Query query = con.query();
con.connect(DATABASE, HOST, USER, PASSWORD);
query << strbuf.str();
StoreQueryResult res = query.store();
cout<<strbuf.str()<<endl;
mysqlpp::Row row;
row = res.at(0);
string formula0(row["formula0"]), formula1(row["formula1"]), formula12(row["formula12"]);
double energy=row["energy"];
double rhoin0=row["rhoin0"];
double rhoin1=row["rhoin1"];
double rhoin12=row["rhoin12"];
double rho0=0.,rho1=0.,rho12=0.;
double beta0=0.,beta1=0.,beta12=0.;
cout<<formula0.size()<<endl;
cout<<"formula0= "<<formula0<<endl;
cout<<"formula1= "<<formula1<<endl;
cout<<"formula12= "<<formula12<<endl;
cout<<"rhoin0= "<<rhoin0<<endl;
cout<<"rhoin1= "<<rhoin1<<endl;
cout<<"rhoin12= "<<rhoin12<<endl;
compound cmpd0(formula0,energy,rhoin0), cmpd1(formula1,energy,rhoin1), cmpd12(formula12,energy,rhoin12);
strbuf.str("");
strbuf << "UPDATE tasks SET rho0="<<cmpd0.rho_el<<",rho1="<<cmpd1.rho_el<<",rho12="<<cmpd12.rho_el<<",beta0="<<cmpd0.beta<<",beta1="<<cmpd1.beta<<",beta12="<<cmpd12.beta<<" WHERE id="<< id;
//cout<<strbuf.str()<<endl;
query.exec(strbuf.str());
cout<<"rho0="<<cmpd0.rho_el<<"\tbeta="<<cmpd0.beta<<endl;
cout<<"rho1="<<cmpd1.rho_el<<"\tbeta="<<cmpd1.beta<<endl;
cout<<"rho12(Maximum)="<<cmpd12.rho_el<<"\tbeta="<<cmpd12.beta<<endl;
}
catch (const BadQuery& er)
{
// Handle any query errors
cerr << "updateDone - Query error: " << er.what() << endl;
return -1;
}
catch (const BadConversion& er)
{
// Handle bad conversions
cerr << "updateDone - Conversion error: " << er.what() << endl <<
"\tretrieved data size: " << er.retrieved <<
", actual size: " << er.actual_size << endl;
return -1;
}
catch (const Exception& er)
{
// Catch-all for any other MySQL++ exceptions
cerr << "updateDone - Error: " << er.what() << endl;
return -1;
}
}
return id;
}
const char* WebModelUnified::website_search(const char* req){
JSONObject root;
JSONArray jsarray;
Connection* conn = connect();
Query query = conn->query();
string reqstr(req);
string reqstr_spaced = replaceChar(reqstr, '+', ' ');
vector<string> splittedstr;
split(splittedstr, reqstr_spaced, boost::algorithm::is_any_of(" "));
int titleForce = 10;
int descriptionForce = 1;
int urlForce = 3;
query << "SELECT * , ";
//Occurences total
for(size_t i1 = 0; i1 < splittedstr.size(); i1++)
{
string s = splittedstr[i1];
if(i1 != 0){
query << " + ";
}
query << "((" <<
titleForce << " * (char_length(title) - char_length(replace(title,'" << s << "',''))) + " <<
descriptionForce << " * (char_length(description) - char_length(replace(description,'" << s << "',''))) + " <<
urlForce << " * (char_length(url) - char_length(replace(url,'" << s << "','')))" <<
") / char_length('" << s << "'))";
}
query << " as Occurances " << " FROM website ";
//Where clause
for(size_t i1 = 0; i1 < splittedstr.size(); i1++)
{
string s = splittedstr[i1];
if(i1 == 0) {
query << "WHERE ";
} else {
query << "OR ";
}
query << "(url LIKE '%" << s << "%' or title LIKE '%" << s << "%' or description LIKE '%" << s << "%') ";
}
query << " ORDER BY " << "Occurances desc, title ASC ";
StoreQueryResult ares = query.store();
unsigned int numrow = ares.num_rows();
for(unsigned int i = 0; i < numrow; i++)
{
JSONObject result;
result[L"title"] = new JSONValue(wchartFromChar(ares[i]["title"]));
result[L"description"] = new JSONValue(wchartFromChar(ares[i]["description"]));
result[L"url"] = new JSONValue(wchartFromChar(ares[i]["url"]));
JSONValue* resultVal = new JSONValue(result);
jsarray.push_back(resultVal);
}
root[L"results"] = new JSONValue(jsarray);
JSONValue* jvalue = new JSONValue(root);
const char* returnStr = fromWString(jvalue->Stringify());
delete jvalue;
return returnStr;
}
void insertIntoDB(int msid, string name, int totalind)
{
int towrite[totalind][10];
float eigen[totalind][5];
try
{
for(int fileno=2; fileno<=10; fileno++)
{
string file = "structout"+toStrings(fileno)+"_f";
ifstream myfile(file.c_str());
if(myfile.is_open())
{
while(! myfile.eof())
{
string line;
getline(myfile, line);
if(line.compare("Inferred ancestry of individuals:")==0)
{
getline(myfile, line);
cout<<"found ::: Infere "<<endl;
break;
}
}
if(myfile.eof())
{
cout<<" couldn't found"<<endl;
return;
}
else
{
int linecount=0;
while(! myfile.eof())
{
string line;
getline(myfile, line);
vector<string> tokens;
Tokenize(line, tokens," ");
cout<<"label "<<atoi(tokens[1].data())<<endl;
towrite[linecount][0]=atoi(tokens[1].data());
//vector<string> tokens1;
//Tokenize(tokens[3], tokens1,": ");
//vector<string> tokens22;
//cout<<"tokens1[1] "<<tokens1[1].data()<<"tokens[3] "<<tokens[3].data()<<" "<<tokens[4].data()<<" "<<tokens[5].data()<<endl;
//Tokenize(tokens1[1], tokens22," ");
double maxx = -1;
int maxpopp = -1;
for(int kk=0; kk < fileno; kk++)
{
double perc = atof(tokens[kk+5].data());
if(perc > maxx)
{
cout<<"perc "<<perc<<" "<<maxx<<endl;
maxpopp = kk+1;
maxx = perc;
}
}
cout<<"pop "<<maxpopp<<endl;
//towrite[linecount][fileno-1]=atoi(tokens1[0].data());
towrite[linecount][fileno-1]=maxpopp;
linecount++;
if(linecount==totalind)
break;
}
}
}
else
{
cout<<"file not found: "<<file <<endl;
return;
}
}
string file = "eig_coef";
ifstream myfile(file.c_str());
if(myfile.is_open())
{
for(int i=0; i < totalind; i++)
{
string line;
getline(myfile, line);
vector<string> tokens;
Tokenize(line, tokens,"\t");
cout<<"eigen1 "<<atof(tokens[0].data())<<"\teigen2 "<<atof(tokens[1].data())<<"\teigen3 "<<atof(tokens[2].data())<<endl;
eigen[i][0]=atof(tokens[0].data());
eigen[i][1]=atof(tokens[1].data());
eigen[i][2]=atof(tokens[2].data());
eigen[i][3]=atof(tokens[3].data());
eigen[i][4]=atof(tokens[4].data());
}
}
else
{
cout<<"file not found: "<<file <<endl;
return;
}
//insert
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
Query query = conn.query();
query << "SELECT createPopStruct(" << msid<< ",'" <<name << "' ) as id";
StoreQueryResult ares = query.store();
int id;
if(!ares)
{
cerr << query.error() << endl;
return;
}
for(size_t i=0; i < ares.num_rows(); i ++)
{
id = ares[i]["id"];
}
//start inserting
query.reset();
for(int i=0; i < totalind; i++)
{
string qstri;
qstri = "INSERT INTO structure (popstructid, sampleid, pop2,pop3,pop4,pop5,pop6,pop7,pop8,pop9,pop10,eig1,eig2,eig3,eig4,eig5) VALUES (";
qstri.append(toStrings(id));
qstri.append(",");
for(int p=0; p<10; p++)
{
qstri.append(toStrings(towrite[i][p]));
qstri.append(",");
}
for(int p=0; p<4; p++)
{
qstri.append(toStrings(eigen[i][p]));
qstri.append(",");
}
qstri.append(toStrings(eigen[i][4]));
qstri.append(")");
cout<<qstri<<endl;
query << qstri;
query.execute();
cout << query.error() << endl;
query.reset();
}
query.reset();
query << "UPDATE popstruct SET loadcmpt = 1 WHERE id = " << id << ";" << endl;
query.execute();
}
catch(BadQuery er)
{
cerr << "Error: " << er.what() << endl;
}
catch(const BadConversion& er)
{
cerr << "Conversion error: " << er.what() << endl;
}
catch(const Exception& er)
{
cerr << "Error: " << er.what() << endl;
}
}
int main(int argc,char **argv)
{
{
char *ee = getenv("ZT_NETCONF_MYSQL_HOST");
if (!ee) {
fprintf(stderr,"missing environment variable: ZT_NETCONF_MYSQL_HOST\n");
return -1;
}
strcpy(mysqlHost,ee);
ee = getenv("ZT_NETCONF_MYSQL_PORT");
if (!ee)
strcpy(mysqlPort,"3306");
else strcpy(mysqlPort,ee);
ee = getenv("ZT_NETCONF_MYSQL_DATABASE");
if (!ee) {
fprintf(stderr,"missing environment variable: ZT_NETCONF_MYSQL_DATABASE\n");
return -1;
}
strcpy(mysqlDatabase,ee);
ee = getenv("ZT_NETCONF_MYSQL_USER");
if (!ee) {
fprintf(stderr,"missing environment variable: ZT_NETCONF_MYSQL_USER\n");
return -1;
}
strcpy(mysqlUser,ee);
ee = getenv("ZT_NETCONF_MYSQL_PASSWORD");
if (!ee) {
fprintf(stderr,"missing environment variable: ZT_NETCONF_MYSQL_PASSWORD\n");
return -1;
}
strcpy(mysqlPassword,ee);
}
char buf[131072],buf2[131072];
Identity signingIdentity;
std::string dictBuf;
try {
dbCon = new Connection(mysqlDatabase,mysqlHost,mysqlUser,mysqlPassword,(unsigned int)strtol(mysqlPort,(char **)0,10));
if (dbCon->connected()) {
fprintf(stderr,"connected to mysql server successfully\n");
} else {
fprintf(stderr,"unable to connect to database server\n");
return -1;
}
} catch (std::exception &exc) {
fprintf(stderr,"unable to connect to database server: %s\n",exc.what());
return -1;
}
// Send ready message to tell parent that the service is up, and to
// solicit netconf-init.
{
Dictionary response;
response["type"] = "ready";
std::string respm = response.toString();
uint32_t respml = (uint32_t)htonl((uint32_t)respm.length());
stdoutWriteLock.lock();
write(STDOUT_FILENO,&respml,4);
write(STDOUT_FILENO,respm.data(),respm.length());
stdoutWriteLock.unlock();
}
for(;;) {
for(int l=0;l<4;) {
int n = (int)read(STDIN_FILENO,buf + l,4 - l);
if (n < 0) {
fprintf(stderr,"error reading frame size from stdin: %s\n",strerror(errno));
return -1;
}
l += n;
}
unsigned int fsize = (unsigned int)ntohl(*((const uint32_t *)buf));
while (dictBuf.length() < fsize) {
int n = (int)read(STDIN_FILENO,buf,std::min((int)sizeof(buf),(int)(fsize - dictBuf.length())));
if (n < 0) {
fprintf(stderr,"error reading frame from stdin: %s\n",strerror(errno));
return -1;
}
for(int i=0;i<n;++i)
dictBuf.push_back(buf[i]);
}
Dictionary request(dictBuf);
dictBuf = "";
if (!dbCon->connected()) {
fprintf(stderr,"connection to database server lost\n");
return -1;
}
// Check QNetworkConfigRefresh (MEMORY table) and push network
// config refreshes to queued peer/network pairs.
try {
Dictionary to;
{
Query q = dbCon->query();
q << "SELECT DISTINCT LOWER(HEX(Node_id)) AS Node_id,LOWER(HEX(Network_id)) AS Network_id FROM QNetworkConfigRefresh";
StoreQueryResult rs = q.store();
for(unsigned long i=0;i<rs.num_rows();++i) {
std::string &nwids = to[rs[i]["Node_id"].c_str()];
if (nwids.length())
nwids.push_back(',');
nwids.append(rs[i]["Network_id"]);
}
}
{
Query q = dbCon->query();
q << "DELETE FROM QNetworkConfigRefresh";
q.exec();
}
Dictionary response;
response["type"] = "netconf-push";
response["to"] = to.toString();
std::string respm = response.toString();
uint32_t respml = (uint32_t)htonl((uint32_t)respm.length());
stdoutWriteLock.lock();
write(STDOUT_FILENO,&respml,4);
write(STDOUT_FILENO,respm.data(),respm.length());
stdoutWriteLock.unlock();
} catch ( ... ) {}
try {
const std::string &reqType = request.get("type");
if (reqType == "netconf-init") { // initialization to set things like netconf's identity
Identity netconfId(request.get("netconfId"));
if ((netconfId)&&(netconfId.hasPrivate())) {
signingIdentity = netconfId;
fprintf(stderr,"got netconf signing identity: %s\n",signingIdentity.toString(false).c_str());
} else {
fprintf(stderr,"netconfId invalid or lacks private key\n");
return -1;
}
} else if (reqType == "netconf-request") { // NETWORK_CONFIG_REQUEST packet
if (!signingIdentity) {
fprintf(stderr,"no signing identity; missing netconf-init?\n");
return -1;
}
// Deserialize querying peer identity and network ID
Identity peerIdentity(request.get("peerId"));
uint64_t nwid = strtoull(request.get("nwid").c_str(),(char **)0,16);
std::string fromAddr(request.get("from",""));
// Meta-information from node, such as (future) geo-location stuff
Dictionary meta;
if (request.contains("meta"))
meta.fromString(request.get("meta"));
// Check validity of node's identity, ignore request on failure
if (!peerIdentity.locallyValidate()) {
fprintf(stderr,"identity failed validity check: %s\n",peerIdentity.toString(false).c_str());
continue;
}
// Save node's identity if unknown
{
Query q = dbCon->query();
q << "SELECT identity FROM Node WHERE id = " << peerIdentity.address().toInt();
StoreQueryResult rs = q.store();
if (rs.num_rows() > 0) {
if (rs[0]["identity"] != peerIdentity.toString(false)) {
// TODO: handle collisions...
continue;
}
} else {
q = dbCon->query();
q << "INSERT INTO Node (id,creationTime,identity) VALUES (" << peerIdentity.address().toInt() << "," << Utils::now() << "," << quote << peerIdentity.toString(false) << ")";
if (!q.exec()) {
fprintf(stderr,"error inserting Node row for peer %s, aborting netconf request\n",peerIdentity.address().toString().c_str());
continue;
}
// TODO: launch background validation
}
}
// Look up core network information
bool isOpen = false;
unsigned int multicastPrefixBits = 0;
unsigned int multicastDepth = 0;
bool emulateArp = false;
bool emulateNdp = false;
unsigned int arpCacheTtl = 0;
unsigned int ndpCacheTtl = 0;
std::string name;
std::string desc;
{
Query q = dbCon->query();
q << "SELECT name,`desc`,isOpen,multicastPrefixBits,multicastDepth,emulateArp,emulateNdp,arpCacheTtl,ndpCacheTtl FROM Network WHERE id = " << nwid;
StoreQueryResult rs = q.store();
if (rs.num_rows() > 0) {
name = rs[0]["name"].c_str();
desc = rs[0]["desc"].c_str();
isOpen = ((int)rs[0]["isOpen"] > 0);
emulateArp = ((int)rs[0]["emulateArp"] > 0);
emulateNdp = ((int)rs[0]["emulateNdp"] > 0);
arpCacheTtl = (unsigned int)rs[0]["arpCacheTtl"];
ndpCacheTtl = (unsigned int)rs[0]["ndpCacheTtl"];
multicastPrefixBits = (unsigned int)rs[0]["multicastPrefixBits"];
multicastDepth = (unsigned int)rs[0]["multicastDepth"];
} else {
Dictionary response;
response["peer"] = peerIdentity.address().toString();
response["nwid"] = request.get("nwid");
response["type"] = "netconf-response";
response["requestId"] = request.get("requestId");
response["error"] = "OBJ_NOT_FOUND";
std::string respm = response.toString();
uint32_t respml = (uint32_t)htonl((uint32_t)respm.length());
stdoutWriteLock.lock();
write(STDOUT_FILENO,&respml,4);
write(STDOUT_FILENO,respm.data(),respm.length());
stdoutWriteLock.unlock();
continue; // ABORT, wait for next request
}
}
// Check membership if this is a closed network
bool authenticated = true;
if (!isOpen) {
Query q = dbCon->query();
q << "SELECT Node_id FROM NetworkNodes WHERE Network_id = " << nwid << " AND Node_id = " << peerIdentity.address().toInt();
StoreQueryResult rs = q.store();
if (!rs.num_rows()) {
Dictionary response;
response["peer"] = peerIdentity.address().toString();
response["nwid"] = request.get("nwid");
response["type"] = "netconf-response";
response["requestId"] = request.get("requestId");
response["error"] = "ACCESS_DENIED";
std::string respm = response.toString();
uint32_t respml = (uint32_t)htonl((uint32_t)respm.length());
stdoutWriteLock.lock();
write(STDOUT_FILENO,&respml,4);
write(STDOUT_FILENO,respm.data(),respm.length());
stdoutWriteLock.unlock();
authenticated = false;
}
}
// Update most recent activity entry for this peer, also indicating
// whether authentication was successful.
{
if (fromAddr.length()) {
Query q = dbCon->query();
q << "INSERT INTO NetworkActivity (Network_id,Node_id,lastActivityTime,authenticated,lastActivityFrom) VALUES (" << nwid << "," << peerIdentity.address().toInt() << "," << Utils::now() << "," << (authenticated ? 1 : 0) << "," << quote << fromAddr << ") ON DUPLICATE KEY UPDATE lastActivityTime = VALUES(lastActivityTime),authenticated = VALUES(authenticated),lastActivityFrom = VALUES(lastActivityFrom)";
q.exec();
} else {
Query q = dbCon->query();
q << "INSERT INTO NetworkActivity (Network_id,Node_id,lastActivityTime,authenticated) VALUES (" << nwid << "," << peerIdentity.address().toInt() << "," << Utils::now() << "," << (authenticated ? 1 : 0) << ") ON DUPLICATE KEY UPDATE lastActivityTime = VALUES(lastActivityTime),authenticated = VALUES(authenticated)";
q.exec();
}
}
if (!authenticated)
continue; // ABORT, wait for next request
// Get list of etherTypes in comma-delimited hex format
std::string etherTypeWhitelist;
{
Query q = dbCon->query();
q << "SELECT DISTINCT LOWER(HEX(etherType)) AS etherType FROM NetworkEthertypes WHERE Network_id = " << nwid;
StoreQueryResult rs = q.store();
for(unsigned long i=0;i<rs.num_rows();++i) {
if (etherTypeWhitelist.length() > 0)
etherTypeWhitelist.push_back(',');
etherTypeWhitelist.append(rs[i]["etherType"].c_str());
}
}
// Get multicast group rates in dictionary format
Dictionary multicastRates;
{
Query q = dbCon->query();
q << "SELECT DISTINCT multicastGroupMac,multicastGroupAdi,preload,maxBalance,accrual FROM NetworkMulticastRates WHERE Network_id = " << nwid;
StoreQueryResult rs = q.store();
for(unsigned long i=0;i<rs.num_rows();++i) {
unsigned long preload = (unsigned long)rs[i]["preload"];
unsigned long maxBalance = (unsigned long)rs[i]["maxBalance"];
unsigned long accrual = (unsigned long)rs[i]["accrual"];
unsigned long long mac = (unsigned long long)rs[i]["multicastGroupMac"];
sprintf(buf,"%.12llx/%lx",(mac & 0xffffffffffffULL),(unsigned long)rs[i]["multicastGroupAdi"]);
sprintf(buf2,"%lx,%lx,%lx",preload,maxBalance,accrual);
multicastRates[buf] = buf2;
}
}
// Check for (or assign?) static IP address assignments
std::string ipv4Static;
std::string ipv6Static;
{
Query q = dbCon->query();
q << "SELECT INET_NTOA(ip) AS ip,netmaskBits FROM IPv4Static WHERE Node_id = " << peerIdentity.address().toInt() << " AND Network_id = " << nwid;
StoreQueryResult rs = q.store();
if (rs.num_rows() > 0) {
for(int i=0;i<rs.num_rows();++i) {
if (ipv4Static.length())
ipv4Static.push_back(',');
ipv4Static.append(rs[i]["ip"].c_str());
ipv4Static.push_back('/');
ipv4Static.append(rs[i]["netmaskBits"].c_str());
}
}
// Try to auto-assign if there's any auto-assign networks with space
// available.
if (!ipv4Static.length()) {
unsigned char addressBytes[5];
peerIdentity.address().copyTo(addressBytes,5);
q = dbCon->query();
q << "SELECT ipNet,netmaskBits FROM IPv4AutoAssign WHERE Network_id = " << nwid;
rs = q.store();
if (rs.num_rows() > 0) {
for(int aaRow=0;aaRow<rs.num_rows();++aaRow) {
uint32_t ipNet = (uint32_t)((unsigned long)rs[aaRow]["ipNet"]);
unsigned int netmaskBits = (unsigned int)rs[aaRow]["netmaskBits"];
uint32_t tryIp = (((uint32_t)addressBytes[1]) << 24) |
(((uint32_t)addressBytes[2]) << 16) |
(((uint32_t)addressBytes[3]) << 8) |
((((uint32_t)addressBytes[4]) % 254) + 1);
tryIp &= (0xffffffff >> netmaskBits);
tryIp |= ipNet;
for(int k=0;k<100000;++k) {
Query q2 = dbCon->query();
q2 << "INSERT INTO IPv4Static (Network_id,Node_id,ip,netmaskBits) VALUES (" << nwid << "," << peerIdentity.address().toInt() << "," << tryIp << "," << netmaskBits << ")";
if (q2.exec()) {
sprintf(buf,"%u.%u.%u.%u",(unsigned int)((tryIp >> 24) & 0xff),(unsigned int)((tryIp >> 16) & 0xff),(unsigned int)((tryIp >> 8) & 0xff),(unsigned int)(tryIp & 0xff));
if (ipv4Static.length())
ipv4Static.push_back(',');
ipv4Static.append(buf);
ipv4Static.push_back('/');
sprintf(buf,"%u",netmaskBits);
ipv4Static.append(buf);
break;
} else { // insert will fail if IP is in use due to uniqueness constraints in DB
++tryIp;
if ((tryIp & 0xff) == 0)
tryIp |= 1;
tryIp &= (0xffffffff >> netmaskBits);
tryIp |= ipNet;
}
}
if (ipv4Static.length())
break;
}
}
}
}
// Assemble response dictionary to send to peer
Dictionary netconf;
sprintf(buf,"%.16llx",(unsigned long long)nwid);
netconf[ZT_NETWORKCONFIG_DICT_KEY_NETWORK_ID] = buf;
netconf[ZT_NETWORKCONFIG_DICT_KEY_ISSUED_TO] = peerIdentity.address().toString();
netconf[ZT_NETWORKCONFIG_DICT_KEY_NAME] = name;
netconf[ZT_NETWORKCONFIG_DICT_KEY_DESC] = desc;
netconf[ZT_NETWORKCONFIG_DICT_KEY_IS_OPEN] = (isOpen ? "1" : "0");
netconf[ZT_NETWORKCONFIG_DICT_KEY_ALLOWED_ETHERNET_TYPES] = etherTypeWhitelist;
netconf[ZT_NETWORKCONFIG_DICT_KEY_MULTICAST_RATES] = multicastRates.toString();
sprintf(buf,"%llx",(unsigned long long)Utils::now());
netconf[ZT_NETWORKCONFIG_DICT_KEY_TIMESTAMP] = buf;
netconf[ZT_NETWORKCONFIG_DICT_KEY_EMULATE_ARP] = (emulateArp ? "1" : "0");
netconf[ZT_NETWORKCONFIG_DICT_KEY_EMULATE_NDP] = (emulateNdp ? "1" : "0");
if (arpCacheTtl) {
sprintf(buf,"%x",arpCacheTtl);
netconf[ZT_NETWORKCONFIG_DICT_KEY_ARP_CACHE_TTL] = buf;
}
if (ndpCacheTtl) {
sprintf(buf,"%x",ndpCacheTtl);
netconf[ZT_NETWORKCONFIG_DICT_KEY_NDP_CACHE_TTL] = buf;
}
if (multicastPrefixBits) {
sprintf(buf,"%x",multicastPrefixBits);
netconf[ZT_NETWORKCONFIG_DICT_KEY_MULTICAST_PREFIX_BITS] = buf;
}
if (multicastDepth) {
sprintf(buf,"%x",multicastDepth);
netconf[ZT_NETWORKCONFIG_DICT_KEY_MULTICAST_DEPTH] = buf;
}
if (ipv4Static.length())
netconf[ZT_NETWORKCONFIG_DICT_KEY_IPV4_STATIC] = ipv4Static;
if (ipv6Static.length())
netconf[ZT_NETWORKCONFIG_DICT_KEY_IPV6_STATIC] = ipv6Static;
if ((!isOpen)&&(authenticated)) {
CertificateOfMembership com(Utils::now(),ZT_NETWORK_AUTOCONF_DELAY * 3,nwid,peerIdentity.address());
com.sign(signingIdentity);
netconf[ZT_NETWORKCONFIG_DICT_KEY_CERTIFICATE_OF_MEMBERSHIP] = com.toString();
}
// Send netconf as service bus response
{
Dictionary response;
response["peer"] = peerIdentity.address().toString();
response["nwid"] = request.get("nwid");
response["type"] = "netconf-response";
response["requestId"] = request.get("requestId");
response["netconf"] = netconf.toString();
std::string respm = response.toString();
uint32_t respml = (uint32_t)htonl((uint32_t)respm.length());
stdoutWriteLock.lock();
write(STDOUT_FILENO,&respml,4);
write(STDOUT_FILENO,respm.data(),respm.length());
stdoutWriteLock.unlock();
// LOOP, wait for next request
}
}
int writeMarkerFile(string mask, string filename)
{
int noidis = 0;
try
{
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
Query query = conn.query();
query << "Select get_ms_id('"<<mask<<"') as id";
StoreQueryResult ares = query.store();
int id;
if(!ares)
{
cerr<<query.error()<<endl;
return -1;
}
for(size_t i = 0; i<ares.num_rows(); i++)
{
id = ares[i]["id"];
//cout << id << endl;
}
query.reset();
//cout << "ID" << id << endl;
query << "SELECT id FROM marker WHERE markersetid= " << id << " ORDER BY idx";
//cout << query.str() << endl;
ares = query.store();
if(!ares)
{
cerr << "Right here. " << endl;
cerr << query.error()<<endl;
return -1;
}
else
{
//run here query once to get size of samples and than store it in a 2d int array
Query q3 = conn.query();
q3 << "SELECT value FROM markerval" << team << ", marker WHERE markerid = marker.id AND markerid = " << ares [0]["id"] << " ORDER BY idx";
StoreQueryResult ares3 = q3.store();
int totalind= ares3.num_rows();
int totalmark = ares.num_rows();
q3.reset();
double towrite[totalind][totalmark];
ofstream myfile;
myfile.open(filename.c_str());
ofstream myfile11;
string fn = "data.vocab";
myfile11.open(fn.c_str());
noidis = ares.num_rows();
for (size_t i = 0; i <ares.num_rows(); i++)
{
myfile11 << ares[i]["id"] << "\n";
Query q2 = conn.query();
q2 << "SELECT value FROM markerval" << team << ", marker WHERE markerid = marker.id AND markerid = " << ares [i]["id"] << " ORDER BY idx";
//cout << q2.str() << endl;
StoreQueryResult ares2 = q2.store();
// noidis = ares2.num_rows();
//cout << noidis << endl;
for(size_t j = 0; j <ares2.num_rows(); j ++)
{
towrite[j][i] = (double)ares2[j]["value"] ;
//myfile << ares2[j]["value"] << "\t";
}
//myfile << endl;
q2.reset();
}
myfile11.close();
for(int ind=0; ind <totalind ; ind++ )
{
for(int mark=0; mark<totalmark; mark++)
{
myfile << towrite[ind][mark] << "\t";
}
myfile << endl;
}
myfile.close();
}
}
catch(BadQuery er)
{
cerr << "Error: " << er.what() << endl;
return -1;
}
catch(const BadConversion& er)
{
cerr << "Conversion error " << er.what() << endl;
return -1;
}
catch(const Exception& er)
{
cerr << "Error :" << er.what() << endl;
return -1;
}
//cout << noidis;
return noidis;
}
int writeTraitFile(string mask)
{
int noidis = 0;
int tts=-1;
try
{
ifstream sqlparmfile("../exe/SQLparms.txt");
string servername, dbname, username, password;
getline(sqlparmfile,servername);
getline(sqlparmfile,dbname);
getline(sqlparmfile,username);
getline(sqlparmfile,password);
Connection conn( dbname.c_str(), servername.c_str(), username.c_str(), password.c_str());
Query query = conn.query();
query << "SELECT get_ts_id('" << mask << "') as id";
StoreQueryResult ares = query.store();
int id;
if(!ares)
{
cerr << query.error() << endl;
return -1;
}
for(size_t i=0; i < ares.num_rows(); i ++)
{
id = ares[i]["id"];
}
query.reset();
query << "SELECT id FROM trait WHERE traitsetid = " << id << " ORDER BY idx";
ares = query.store();
if(!ares)
{
cerr << query.error() << endl;
return -1;
}
else
{
tts = ares.num_rows();
int fnum=1;
ofstream myfile1;
string fname1 = "tr_id";
myfile1.open(fname1.c_str());
for(size_t i = 0; i < ares.num_rows(); i ++)
{
ofstream myfile;
string fname = "tr"+toStrings(fnum);
myfile.open(fname.c_str());
Query q2 = conn.query();
myfile1 << ares[i]["id"] << "\n";
query << "SELECT value FROM traitval" << team << ",trait WHERE traitid=trait.id AND traitid = " << ares[i]["id"] << " ORDER BY idx";
StoreQueryResult ares2 = query.store();
noidis = ares2.num_rows();
for(size_t j = 0; j < ares2.num_rows(); j ++)
{
myfile << ares2[j]["value"] << "\n";
}
myfile << endl;
q2.reset();
myfile.close();
fnum++;
}
myfile1.close();
}
}
catch(BadQuery er)
{
cerr << "Error: " << er.what() << endl;
return -1;
}
catch(const BadConversion& er)
{
cerr << "Conversion error: " << er.what() << endl;
return -1;
}
catch(const Exception& er)
{
cerr << "Error: " << er.what() << endl;
return -1;
}
return tts;
}
int main(int argc, char* argv[])
{
Connection c("magpie", "localhost", "stephen",
"iloverae", 0);
ifstream ifs;
ifs.open(argv[1]);
string junk, email, firstName, lastName, userName;
int sectionNum = argv[1][3] - 48;
Query q = c.query();
Query r = c.query();
Query s = c.query();
Query t = c.query();
while (ifs.peek() != EOF)
{
int uid;
try
{
getline (ifs, junk, ':');
getline (ifs, email, '"');
userName = email;
userName.erase(userName.find_first_of('@'));
getline (ifs, junk, '"');
getline (ifs, firstName, ' ');
getline (ifs, lastName, '"');
getline (ifs, junk);
if (lastName[2] == ' ') {
lastName.erase(0,3);
}
if (lastName[1] == '\'') {
lastName.erase(1,1);
}
//
// Check and see whether user already exists.
s << "SELECT * FROM user WHERE username='******'" << endl;
StoreQueryResult uqr = s.store();
if (uqr.num_rows() <= 0) {
cout << "Creating student account for " << email << " " << userName << " " << firstName << " " << lastName << endl;
q << "INSERT INTO user (username,password,firstname,lastname,role) VALUES ('" << userName << "', SHA1('" << userName << "'), '" << firstName << "','" << lastName << "','student')" << endl;
q.execute();
r << "SELECT last_insert_id()" << endl;
StoreQueryResult lid = r.store();
uid = lid[0][0];
}
else {
cout << "(user " << userName << " already in database.)" << endl;
uid = uqr[0]["uid"];
}
t << "INSERT INTO courseLink (uid,courseid) VALUES (" << uid << ", " << sectionNum << ")" << endl;
t.execute();
q.reset();
r.reset();
s.reset();
t.reset();
}
catch (const Exception &e)
{
cout << "I just caught error: " << e.what() << endl;
exit(1);
}
}
c.disconnect();
return 0;
}